I have come across a number of cases where the Geodatabase object has an empty collection of GeodatabaseFeatureTables. I have gone back and recreated everything from scratch, sometimes I have seen it fix the issues others not. When generating these replicas everything goes fine, I have checked Server logs and these only contain debug/info messages. Nothing indicative of errors. I can open the databases in DB Browser for SQLLite and everything looks fine.
After a bunch of research I have found one difference. The databases that work all seem to have a table called GDB_ServiceItems. The databases that show no layers none appear to have this table.
So a question, would this table missing cause the API to behave in this manner? Does the initialization of the Geodatabase object look to this table for information about the tables?